[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1305.5323"}],"publisher":"American Physical Society","publist_id":"4627","abstract":[{"text":"We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability.","lang":"eng"}],"_id":"2300","type":"journal_article","month":"08","author":[{"last_name":"Giuliani","first_name":"Alessandro","full_name":"Giuliani, Alessandro"},{"full_name":"Lieb, Élliott","first_name":"Élliott","last_name":"Lieb"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"language":[{"iso":"eng"}],"publication":"Physical Review B","scopus_import":1,"volume":88,"date_created":"2018-12-11T11:56:51Z","department":[{"_id":"RoSe"}],"oa_version":"Preprint","date_published":"2013-08-01T00:00:00Z","publication_status":"published","citation":{"ista":"Giuliani A, Lieb É, Seiringer R. 2013. Realization of stripes and slabs in two and three dimensions. Physical Review B. 88(6), 064401.","ieee":"A. Giuliani, É. Lieb, and R. Seiringer, “Realization of stripes and slabs in two and three dimensions,” <i>Physical Review B</i>, vol. 88, no. 6. American Physical Society, 2013.","mla":"Giuliani, Alessandro, et al. “Realization of Stripes and Slabs in Two and Three Dimensions.” <i>Physical Review B</i>, vol. 88, no. 6, 064401, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevB.88.064401\">10.1103/PhysRevB.88.064401</a>.","short":"A. Giuliani, É. Lieb, R. Seiringer, Physical Review B 88 (2013).","chicago":"Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Realization of Stripes and Slabs in Two and Three Dimensions.” <i>Physical Review B</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevB.88.064401\">https://doi.org/10.1103/PhysRevB.88.064401</a>.","apa":"Giuliani, A., Lieb, É., &#38; Seiringer, R. (2013). Realization of stripes and slabs in two and three dimensions. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.88.064401\">https://doi.org/10.1103/PhysRevB.88.064401</a>","ama":"Giuliani A, Lieb É, Seiringer R. Realization of stripes and slabs in two and three dimensions. <i>Physical Review B</i>. 2013;88(6). doi:<a href=\"https://doi.org/10.1103/PhysRevB.88.064401\">10.1103/PhysRevB.88.064401</a>"},"quality_controlled":"1","arxiv":1,"oa":1,"external_id":{"arxiv":["1305.5323"]},"date_updated":"2021-01-12T06:56:38Z","intvolume":"        88","status":"public","title":"Realization of stripes and slabs in two and three dimensions","issue":"6","doi":"10.1103/PhysRevB.88.064401","day":"01","article_number":"064401","year":"2013"},{"scopus_import":1,"status":"public","date_updated":"2021-01-12T06:56:38Z","publication":"Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation","type":"conference","language":[{"iso":"eng"}],"conference":{"start_date":"2013-06-16","end_date":"2013-06-19","location":"Seattle, WA, United States","name":"PLDI: Programming Languages Design and Implementation"},"month":"06","author":[{"first_name":"Ankush","full_name":"Desai, Ankush","last_name":"Desai"},{"last_name":"Gupta","first_name":"Vivek","full_name":"Gupta, Vivek"},{"full_name":"Jackson, Ethan","first_name":"Ethan","last_name":"Jackson"},{"full_name":"Qadeer, Shaz","first_name":"Shaz","last_name":"Qadeer"},{"last_name":"Rajamani","first_name":"Sriram","full_name":"Rajamani, Sriram"},{"orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien","first_name":"Damien","last_name":"Zufferey"}],"date_created":"2018-12-11T11:56:52Z","year":"2013","page":"321 - 331","doi":"10.1145/2491956.2462184","day":"01","title":"P: Safe asynchronous event-driven programming","publist_id":"4626","date_published":"2013-06-01T00:00:00Z","ec_funded":1,"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"main_file_link":[{"url":"http://research.microsoft.com/pubs/191069/pldi212_desai.pdf"}],"oa_version":"None","publisher":"ACM","department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2301","quality_controlled":"1","abstract":[{"text":"We describe the design and implementation of P, a domain-specific language to write asynchronous event driven code. P allows the programmer to specify the system as a collection of interacting state machines, which communicate with each other using events. P unifies modeling and programming into one activity for the programmer. Not only can a P program be compiled into executable code, but it can also be tested using model checking techniques. P allows the programmer to specify the environment, used to &quot;close&quot; the system during testing, as nondeterministic ghost machines. Ghost machines are erased during compilation to executable code; a type system ensures that the erasure is semantics preserving. The P language is designed so that a P program can be checked for responsiveness-the ability to handle every event in a timely manner. By default, a machine needs to handle every event that arrives in every state. But handling every event in every state is impractical. The language provides a notion of deferred events where the programmer can annotate when she wants to delay processing an event. The default safety checker looks for presence of unhan-dled events. The language also provides default liveness checks that an event cannot be potentially deferred forever. P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P.","lang":"eng"}],"citation":{"apa":"Desai, A., Gupta, V., Jackson, E., Qadeer, S., Rajamani, S., &#38; Zufferey, D. (2013). P: Safe asynchronous event-driven programming. In <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i> (pp. 321–331). Seattle, WA, United States: ACM. <a href=\"https://doi.org/10.1145/2491956.2462184\">https://doi.org/10.1145/2491956.2462184</a>","ama":"Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. P: Safe asynchronous event-driven programming. In: <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>. ACM; 2013:321-331. doi:<a href=\"https://doi.org/10.1145/2491956.2462184\">10.1145/2491956.2462184</a>","chicago":"Desai, Ankush, Vivek Gupta, Ethan Jackson, Shaz Qadeer, Sriram Rajamani, and Damien Zufferey. “P: Safe Asynchronous Event-Driven Programming.” In <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, 321–31. ACM, 2013. <a href=\"https://doi.org/10.1145/2491956.2462184\">https://doi.org/10.1145/2491956.2462184</a>.","ieee":"A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, and D. Zufferey, “P: Safe asynchronous event-driven programming,” in <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, Seattle, WA, United States, 2013, pp. 321–331.","short":"A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, D. Zufferey, in:, Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–331.","mla":"Desai, Ankush, et al. “P: Safe Asynchronous Event-Driven Programming.” <i>Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, ACM, 2013, pp. 321–31, doi:<a href=\"https://doi.org/10.1145/2491956.2462184\">10.1145/2491956.2462184</a>.","ista":"Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. 2013. P: Safe asynchronous event-driven programming. Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Languages Design and Implementation, 321–331."},"publication_status":"published"},{"doi":"10.1007/s11515-013-1279-6","day":"03","issue":"6","title":"Dissection of gene function at clonal level using mosaic analysis with double markers","volume":8,"date_created":"2018-12-11T11:56:52Z","year":"2013","page":"557 - 568","type":"journal_article","month":"09","author":[{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"language":[{"iso":"eng"}],"intvolume":"         8","scopus_import":1,"status":"public","publication":"Frontiers in Biology","date_updated":"2021-01-12T06:56:39Z","abstract":[{"text":"MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools.","lang":"eng"}],"citation":{"ieee":"S. Hippenmeyer, “Dissection of gene function at clonal level using mosaic analysis with double markers,” <i>Frontiers in Biology</i>, vol. 8, no. 6. Springer, pp. 557–568, 2013.","mla":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” <i>Frontiers in Biology</i>, vol. 8, no. 6, Springer, 2013, pp. 557–68, doi:<a href=\"https://doi.org/10.1007/s11515-013-1279-6\">10.1007/s11515-013-1279-6</a>.","short":"S. Hippenmeyer, Frontiers in Biology 8 (2013) 557–568.","ista":"Hippenmeyer S. 2013. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 8(6), 557–568.","apa":"Hippenmeyer, S. (2013). Dissection of gene function at clonal level using mosaic analysis with double markers. <i>Frontiers in Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11515-013-1279-6\">https://doi.org/10.1007/s11515-013-1279-6</a>","ama":"Hippenmeyer S. Dissection of gene function at clonal level using mosaic analysis with double markers. <i>Frontiers in Biology</i>. 2013;8(6):557-568. doi:<a href=\"https://doi.org/10.1007/s11515-013-1279-6\">10.1007/s11515-013-1279-6</a>","chicago":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” <i>Frontiers in Biology</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s11515-013-1279-6\">https://doi.org/10.1007/s11515-013-1279-6</a>."},"publication_status":"published","acknowledgement":"This work was supported by IST Austria institutional funds.","_id":"2303","quality_controlled":"1","publisher":"Springer","oa_version":"None","department":[{"_id":"SiHi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"4624","article_type":"review","date_published":"2013-09-03T00:00:00Z"},{"date_updated":"2021-01-12T06:56:39Z","publication":"Electronic Notes in Discrete Mathematics","intvolume":"        43","scopus_import":1,"status":"public","type":"journal_article","month":"09","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pausinger, Florian","last_name":"Pausinger"}],"page":"43 - 50","date_created":"2018-12-11T11:56:53Z","year":"2013","title":"Van der Corput sequences and linear permutations","volume":43,"day":"05","doi":"10.1016/j.endm.2013.07.008","date_published":"2013-09-05T00:00:00Z","publist_id":"4623","department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","oa_version":"None","quality_controlled":"1","acknowledgement":"This research is supported by the Graduate school of IST Austria (Institute of Science and Technology Austria).","_id":"2304","abstract":[{"text":"This extended abstract is concerned with the irregularities of distribution of one-dimensional permuted van der Corput sequences that are generated from linear permutations. We show how to obtain upper bounds for the discrepancy and diaphony of these sequences, by relating them to Kronecker sequences and applying earlier results of Faure and Niederreiter.","lang":"eng"}],"citation":{"ama":"Pausinger F. Van der Corput sequences and linear permutations. <i>Electronic Notes in Discrete Mathematics</i>. 2013;43:43-50. doi:<a href=\"https://doi.org/10.1016/j.endm.2013.07.008\">10.1016/j.endm.2013.07.008</a>","apa":"Pausinger, F. (2013). Van der Corput sequences and linear permutations. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2013.07.008\">https://doi.org/10.1016/j.endm.2013.07.008</a>","chicago":"Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.endm.2013.07.008\">https://doi.org/10.1016/j.endm.2013.07.008</a>.","ieee":"F. Pausinger, “Van der Corput sequences and linear permutations,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 43. Elsevier, pp. 43–50, 2013.","short":"F. Pausinger, Electronic Notes in Discrete Mathematics 43 (2013) 43–50.","mla":"Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 43, Elsevier, 2013, pp. 43–50, doi:<a href=\"https://doi.org/10.1016/j.endm.2013.07.008\">10.1016/j.endm.2013.07.008</a>.","ista":"Pausinger F. 2013. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 43, 43–50."},"publication_status":"published"},{"related_material":{"record":[{"id":"1294","relation":"later_version","status":"public"}]},"page":"331 - 340","date_created":"2018-12-11T11:56:53Z","type":"conference","author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Forejt","full_name":"Forejt, Vojtěch","first_name":"Vojtěch"},{"last_name":"Kučera","full_name":"Kučera, Antonín","first_name":"Antonín"}],"language":[{"iso":"eng"}],"month":"08","conference":{"name":"LICS: Logic in Computer Science","location":"New Orleans, LA, United States","end_date":"2013-06-28","start_date":"2013-06-25"},"publication":"28th Annual ACM/IEEE Symposium","scopus_import":1,"abstract":[{"lang":"eng","text":"We study the complexity of central controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize both the expected mean-payoff performance of the system and its stability. e argue that the basic theoretical notion of expressing the stability in terms of the variance of the mean-payoff (called global variance in our paper) is not always sufficient, since it ignores possible instabilities on respective runs. For this reason we propose alernative definitions of stability, which we call local and hybrid variance, and which express how rewards on each run deviate from the run's own mean-payoff and from the expected mean-payoff, respectively. We show that a strategy ensuring both the expected mean-payoff and the variance below given bounds requires randomization and memory, under all the above semantics of variance. We then look at the problem of determining whether there is a such a strategy. For the global variance, we show that the problem is in PSPACE, and that the answer can be approximated in pseudo-polynomial time. For the hybrid variance, the analogous decision problem is in NP, and a polynomial-time approximating algorithm also exists. For local variance, we show that the decision problem is in NP. Since the overall performance can be traded for stability (and vice versa), we also present algorithms for approximating the associated Pareto curve in all the three cases. Finally, we study a special case of the decision problems, where we require a given expected mean-payoff together with zero variance. Here we show that the problems can be all solved in polynomial time."}],"_id":"2305","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1305.4103"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publisher":"IEEE","ec_funded":1,"publist_id":"4622","title":"Trading performance for stability in Markov decision processes","doi":"10.1109/LICS.2013.39","day":"01","year":"2013","oa":1,"external_id":{"arxiv":["1305.4103"]},"date_updated":"2023-09-20T11:15:30Z","status":"public","citation":{"ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2013. Trading performance for stability in Markov decision processes. 28th Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 331–340.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” in <i>28th Annual ACM/IEEE Symposium</i>, New Orleans, LA, United States, 2013, pp. 331–340.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, in:, 28th Annual ACM/IEEE Symposium, IEEE, 2013, pp. 331–340.","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>28th Annual ACM/IEEE Symposium</i>, IEEE, 2013, pp. 331–40, doi:<a href=\"https://doi.org/10.1109/LICS.2013.39\">10.1109/LICS.2013.39</a>.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” In <i>28th Annual ACM/IEEE Symposium</i>, 331–40. IEEE, 2013. <a href=\"https://doi.org/10.1109/LICS.2013.39\">https://doi.org/10.1109/LICS.2013.39</a>.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. In: <i>28th Annual ACM/IEEE Symposium</i>. IEEE; 2013:331-340. doi:<a href=\"https://doi.org/10.1109/LICS.2013.39\">10.1109/LICS.2013.39</a>","apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2013). Trading performance for stability in Markov decision processes. In <i>28th Annual ACM/IEEE Symposium</i> (pp. 331–340). New Orleans, LA, United States: IEEE. <a href=\"https://doi.org/10.1109/LICS.2013.39\">https://doi.org/10.1109/LICS.2013.39</a>"},"publication_status":"published","quality_controlled":"1","arxiv":1,"department":[{"_id":"KrCh"}],"oa_version":"Preprint","date_published":"2013-08-01T00:00:00Z"},{"date_created":"2018-12-11T11:56:53Z","volume":50,"ddc":["020"],"file_date_updated":"2020-07-14T12:45:38Z","article_processing_charge":"No","language":[{"iso":"ger"}],"author":[{"orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","full_name":"Danowski, Patrick","first_name":"Patrick"},{"last_name":"Pohl","first_name":"Adrian","full_name":"Pohl, Adrian"}],"month":"09","type":"book","_id":"2306","alternative_title":["Bibliotheks- und Informationspraxis"],"abstract":[{"lang":"ger","text":"Das Buch ist sowohl eine Einführung in die Themen Linked Data, Open Data und Open Linked Data als es auch den konkreten Bezug auf Bibliotheken behandelt. Hierzu werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement, die noch nicht mit dem Thema vertraut sind."}],"publist_id":"4621","publisher":"De Gruyter","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2013","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1515/9783110278736","day":"13","has_accepted_license":"1","title":"(Open) Linked Data in Bibliotheken","publication_identifier":{"issn":["2191-3587"],"eisbn":["9-783-1102-7873-6"],"isbn":[" 978-3-11-027634-3"]},"status":"public","intvolume":"        50","pubrep_id":"725","date_updated":"2021-12-21T12:17:19Z","oa":1,"quality_controlled":"1","citation":{"ista":"Danowski P, Pohl A. 2013. (Open) Linked Data in Bibliotheken, De Gruyter,p.","ieee":"P. Danowski and A. Pohl, <i>(Open) Linked Data in Bibliotheken</i>, vol. 50. De Gruyter, 2013.","mla":"Danowski, Patrick, and Adrian Pohl. <i>(Open) Linked Data in Bibliotheken</i>. Vol. 50, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/9783110278736\">10.1515/9783110278736</a>.","short":"P. Danowski, A. Pohl, (Open) Linked Data in Bibliotheken, De Gruyter, 2013.","chicago":"Danowski, Patrick, and Adrian Pohl. <i>(Open) Linked Data in Bibliotheken</i>. Vol. 50. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/9783110278736\">https://doi.org/10.1515/9783110278736</a>.","ama":"Danowski P, Pohl A. <i>(Open) Linked Data in Bibliotheken</i>. Vol 50. De Gruyter; 2013. doi:<a href=\"https://doi.org/10.1515/9783110278736\">10.1515/9783110278736</a>","apa":"Danowski, P., &#38; Pohl, A. (2013). <i>(Open) Linked Data in Bibliotheken</i> (Vol. 50). De Gruyter. <a 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The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification. We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved. We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications."}],"publist_id":"4599","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","doi":"10.1007/978-3-642-40184-8_20","day":"01","has_accepted_license":"1","title":"From model checking to model measuring","status":"public","intvolume":"      8052","pubrep_id":"129","date_updated":"2023-02-23T12:25:26Z","oa":1,"quality_controlled":"1","citation":{"chicago":"Henzinger, Thomas A, and Jan Otop. “From Model Checking to Model Measuring.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">https://doi.org/10.1007/978-3-642-40184-8_20</a>.","ama":"Henzinger TA, Otop J. From model checking to model measuring. 2013;8052:273-287. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">10.1007/978-3-642-40184-8_20</a>","apa":"Henzinger, T. A., &#38; Otop, J. (2013). From model checking to model measuring. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Springer. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">https://doi.org/10.1007/978-3-642-40184-8_20</a>","ista":"Henzinger TA, Otop J. 2013. From model checking to model measuring. 8052, 273–287.","mla":"Henzinger, Thomas A., and Jan Otop. <i>From Model Checking to Model Measuring</i>. Vol. 8052, Springer, 2013, pp. 273–87, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">10.1007/978-3-642-40184-8_20</a>.","short":"T.A. Henzinger, J. Otop, 8052 (2013) 273–287.","ieee":"T. A. Henzinger and J. Otop, “From model checking to model measuring,” vol. 8052. Springer, pp. 273–287, 2013."},"publication_status":"published","date_published":"2013-08-01T00:00:00Z","oa_version":"Submitted Version","file":[{"creator":"system","file_id":"5301","content_type":"application/pdf","date_created":"2018-12-12T10:17:45Z","file_name":"IST-2013-129-v1+1_concur.pdf","access_level":"open_access","relation":"main_file","checksum":"4c04695c4bfdf2119cd4f5d1babc3e8a","file_size":378587,"date_updated":"2020-07-14T12:45:38Z"}],"series_title":"Lecture Notes in Computer Science","department":[{"_id":"ToHe"}]},{"publication_status":"published","citation":{"mla":"Henzinger, Thomas A., et al. <i>Aspect-Oriented Linearizability Proofs</i>. Vol. 8052, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 242–56, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">10.1007/978-3-642-40184-8_18</a>.","short":"T.A. Henzinger, A. Sezgin, V. Vafeiadis, 8052 (2013) 242–256.","ieee":"T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” vol. 8052. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 242–256, 2013.","ista":"Henzinger TA, Sezgin A, Vafeiadis V. 2013. Aspect-oriented linearizability proofs. 8052, 242–256.","apa":"Henzinger, T. A., Sezgin, A., &#38; Vafeiadis, V. (2013). Aspect-oriented linearizability proofs. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">https://doi.org/10.1007/978-3-642-40184-8_18</a>","ama":"Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. 2013;8052:242-256. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">10.1007/978-3-642-40184-8_18</a>","chicago":"Henzinger, Thomas A, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Lecture Notes in Computer Science. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">https://doi.org/10.1007/978-3-642-40184-8_18</a>."},"quality_controlled":"1","department":[{"_id":"ToHe"}],"oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:39Z","file_name":"IST-2014-197-v1+1_main-queue-verification.pdf","relation":"main_file","access_level":"open_access","file_size":337059,"checksum":"bdbb520de91751fe0136309ad4ef67e4","file_id":"4721","content_type":"application/pdf","date_created":"2018-12-12T10:08:58Z","creator":"system"}],"series_title":"Lecture Notes in Computer Science","date_published":"2013-08-01T00:00:00Z","title":"Aspect-oriented linearizability proofs","has_accepted_license":"1","day":"01","doi":"10.1007/978-3-642-40184-8_18","year":"2013","oa":1,"pubrep_id":"197","date_updated":"2023-02-23T10:16:27Z","status":"public","intvolume":"      8052","abstract":[{"lang":"eng","text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates.\r\nIn response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof."}],"_id":"2328","alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"}],"ec_funded":1,"publist_id":"4598","volume":8052,"ddc":["000","004"],"file_date_updated":"2020-07-14T12:45:39Z","related_material":{"record":[{"status":"public","id":"1832","relation":"later_version"}]},"page":"242 - 256","date_created":"2018-12-11T11:57:01Z","month":"08","language":[{"iso":"eng"}],"conference":{"end_date":"2013-08-30","start_date":"2013-08-27","location":"Buenos Aires, Argentina","name":"CONCUR: Concurrency Theory"},"author":[{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Ali","full_name":"Sezgin, Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vafeiadis","full_name":"Vafeiadis, Viktor","first_name":"Viktor"}],"type":"conference","scopus_import":1},{"intvolume":"      8052","status":"public","date_updated":"2023-02-23T13:00:42Z","external_id":{"arxiv":["1210.3141"]},"oa":1,"year":"2013","day":"01","doi":"10.1007/978-3-642-40184-8_35","title":"Hyperplane separation technique for multidimensional mean-payoff games","date_published":"2013-08-01T00:00:00Z","series_title":"Lecture Notes in Computer Science","oa_version":"Preprint","department":[{"_id":"KrCh"}],"quality_controlled":"1","arxiv":1,"publication_status":"published","citation":{"apa":"Chatterjee, K., &#38; Velner, Y. (2013). Hyperplane separation technique for multidimensional mean-payoff games. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentinia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">https://doi.org/10.1007/978-3-642-40184-8_35</a>","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. 2013;8052:500-515. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">10.1007/978-3-642-40184-8_35</a>","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">https://doi.org/10.1007/978-3-642-40184-8_35</a>.","mla":"Chatterjee, Krishnendu, and Yaron Velner. <i>Hyperplane Separation Technique for Multidimensional Mean-Payoff Games</i>. Vol. 8052, Springer, 2013, pp. 500–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">10.1007/978-3-642-40184-8_35</a>.","short":"K. Chatterjee, Y. Velner, 8052 (2013) 500–515.","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” vol. 8052. Springer, pp. 500–515, 2013.","ista":"Chatterjee K, Velner Y. 2013. Hyperplane separation technique for multidimensional mean-payoff games. 8052, 500–515."},"scopus_import":1,"type":"conference","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"conference":{"location":"Buenos Aires, Argentinia","name":"CONCUR: Concurrency Theory","start_date":"2013-08-27","end_date":"2013-08-30"},"language":[{"iso":"eng"}],"month":"08","date_created":"2018-12-11T11:57:01Z","page":"500 - 515","related_material":{"record":[{"relation":"later_version","id":"717","status":"public"}]},"volume":8052,"publist_id":"4597","ec_funded":1,"main_file_link":[{"url":"http://arxiv.org/abs/1210.3141","open_access":"1"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"_id":"2329","abstract":[{"text":"Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work, we consider both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity games.","lang":"eng"}]},{"quality_controlled":"1","citation":{"chicago":"Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” <i>Genome Announcements</i>. American Society for Microbiology, 2013. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>.","apa":"Fernandes Redondo, R. A., Kupczok, A., Stift, G., &#38; Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>","ama":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. 2013;1(3). doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>","ista":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3).","mla":"Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” <i>Genome Announcements</i>, vol. 1, no. 3, American Society for Microbiology, 2013, doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>.","short":"R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).","ieee":"R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” <i>Genome Announcements</i>, vol. 1, no. 3. American Society for Microbiology, 2013."},"publication_status":"published","date_published":"2013-06-13T00:00:00Z","department":[{"_id":"JoBo"},{"_id":"LifeSc"}],"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:40Z","file_size":130026,"checksum":"0751ec74b695567e0cdf02aaf9c26829","access_level":"open_access","relation":"main_file","file_name":"IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf","date_created":"2018-12-12T10:17:36Z","content_type":"application/pdf","file_id":"5291","creator":"system"}],"year":"2013","issue":"3","title":"Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis","has_accepted_license":"1","doi":"10.1128/genomeA.00216-13","day":"13","pubrep_id":"398","date_updated":"2021-01-12T06:57:19Z","status":"public","intvolume":"         1","oa":1,"_id":"2410","abstract":[{"text":"Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. ","lang":"eng"}],"publist_id":"4516","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Society for Microbiology","date_created":"2018-12-11T11:57:30Z","ddc":["576"],"volume":1,"file_date_updated":"2020-07-14T12:45:40Z","publication":"Genome Announcements","scopus_import":1,"month":"06","author":[{"first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anne","full_name":"Kupczok, Anne","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"id":"2DB195CA-F248-11E8-B48F-1D18A9856A87","first_name":"Gertraud","full_name":"Stift, Gertraud","last_name":"Stift"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback"}],"language":[{"iso":"eng"}],"type":"journal_article"},{"oa":1,"date_updated":"2021-01-12T06:57:20Z","pubrep_id":"397","intvolume":"        13","status":"public","has_accepted_license":"1","issue":"1","title":"Probabilistic models for CRISPR spacer content evolution ","day":"26","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1186/1471-2148-13-54","year":"2013","department":[{"_id":"JoBo"}],"oa_version":"Published Version","file":[{"file_size":518729,"checksum":"029c7e0b198c19312b66ecce3cabb22f","access_level":"open_access","relation":"main_file","file_name":"IST-2015-397-v1+1_1471-2148-13-54.pdf","date_updated":"2020-07-14T12:45:40Z","creator":"system","date_created":"2018-12-12T10:17:15Z","content_type":"application/pdf","file_id":"5268"}],"date_published":"2013-02-26T00:00:00Z","publication_status":"published","citation":{"ista":"Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54.","ieee":"A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013.","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>.","short":"A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.","chicago":"Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>.","apa":"Kupczok, A., &#38; Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>","ama":"Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. 2013;13(1):54-54. doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>"},"quality_controlled":"1","type":"journal_article","month":"02","author":[{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Kupczok, Anne","last_name":"Kupczok"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"}],"language":[{"iso":"eng"}],"publication":"BMC Evolutionary Biology","scopus_import":1,"file_date_updated":"2020-07-14T12:45:40Z","volume":13,"ddc":["576"],"page":"54 - 54","date_created":"2018-12-11T11:57:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"BioMed Central","publist_id":"4514","abstract":[{"text":"Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.","lang":"eng"}],"_id":"2412"},{"date_created":"2018-12-11T11:57:31Z","year":"2013","day":"01","doi":"10.1002/9783527671632.ch08","publication_identifier":{"isbn":["9783527411986 "],"eisbn":["9783527671632"]},"title":"Neuronal oscillations scale up and scale down the brain dynamics ","scopus_import":1,"status":"public","date_updated":"2021-01-12T06:57:20Z","publication":"Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain","type":"book_chapter","author":[{"last_name":"Valderrama","first_name":"Mario","full_name":"Valderrama, Mario"},{"id":"421234E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8790-1914","last_name":"Botella Soler","first_name":"Vicente","full_name":"Botella Soler, Vicente"},{"last_name":"Le Van Quyen","full_name":"Le Van Quyen, Michel","first_name":"Michel"}],"language":[{"iso":"eng"}],"month":"08","alternative_title":["Reviews of Nonlinear Dynamics and Complexity"],"_id":"2413","quality_controlled":"1","abstract":[{"text":"Progress in understanding the global brain dynamics has remained slow to date in large part because of the highly multiscale nature of brain activity. Indeed, normal brain dynamics is characterized by complex interactions between multiple levels: from the microscopic scale of single neurons to the mesoscopic level of local groups of neurons, and finally to the macroscopic level of the whole brain. Among the most difficult tasks are those of identifying which scales are significant for a given particular function and describing how the scales affect each other. It is important to realize that the scales of time and space are linked together, or even intertwined, and that causal inference is far more ambiguous between than within levels. We approach this problem from the perspective of our recent work on simultaneous recording from micro- and macroelectrodes in the human brain. We propose a physiological description of these multilevel interactions, based on phase–amplitude coupling of neuronal oscillations that operate at multiple frequencies and on different spatial scales. Specifically, the amplitude of the oscillations on a particular spatial scale is modulated by phasic variations in neuronal excitability induced by lower frequency oscillations that emerge on a larger spatial scale. Following this general principle, it is possible to scale up or scale down the multiscale brain dynamics. It is expected that large-scale network oscillations in the low-frequency range, mediating downward effects, may play an important role in attention and consciousness.","lang":"eng"}],"citation":{"chicago":"Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” In <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, edited by Misha Meyer and Z. Pesenson. Wiley-VCH, 2013. <a href=\"https://doi.org/10.1002/9783527671632.ch08\">https://doi.org/10.1002/9783527671632.ch08</a>.","ama":"Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>. Wiley-VCH; 2013. doi:<a href=\"https://doi.org/10.1002/9783527671632.ch08\">10.1002/9783527671632.ch08</a>","apa":"Valderrama, M., Botella Soler, V., &#38; Le Van Quyen, M. (2013). Neuronal oscillations scale up and scale down the brain dynamics . In M. Meyer &#38; Z. Pesenson (Eds.), <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>. Wiley-VCH. <a href=\"https://doi.org/10.1002/9783527671632.ch08\">https://doi.org/10.1002/9783527671632.ch08</a>","ista":"Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity, .","ieee":"M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations scale up and scale down the brain dynamics ,” in <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, M. Meyer and Z. Pesenson, Eds. Wiley-VCH, 2013.","short":"M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH, 2013.","mla":"Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, edited by Misha Meyer and Z. Pesenson, Wiley-VCH, 2013, doi:<a href=\"https://doi.org/10.1002/9783527671632.ch08\">10.1002/9783527671632.ch08</a>."},"publication_status":"published","editor":[{"last_name":"Meyer","first_name":"Misha","full_name":"Meyer, Misha"},{"first_name":"Z.","full_name":"Pesenson, Z.","last_name":"Pesenson"}],"publist_id":"4513","date_published":"2013-08-01T00:00:00Z","publisher":"Wiley-VCH","oa_version":"None","department":[{"_id":"GaTk"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"year":"2013","has_accepted_license":"1","title":"Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions","issue":"DEC","doi":"10.3389/fnbeh.2013.00217","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"27","pubrep_id":"953","date_updated":"2021-01-12T08:00:53Z","status":"public","intvolume":"         7","oa":1,"quality_controlled":"1","publication_status":"published","citation":{"short":"D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).","mla":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” <i>Frontiers in Behavioral Neuroscience</i>, vol. 7, no. DEC, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">10.3389/fnbeh.2013.00217</a>.","ieee":"D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions,” <i>Frontiers in Behavioral Neuroscience</i>, vol. 7, no. DEC. Frontiers Research Foundation, 2013.","ista":"Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. Frontiers in Behavioral Neuroscience. 7(DEC).","ama":"Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. <i>Frontiers in Behavioral Neuroscience</i>. 2013;7(DEC). doi:<a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">10.3389/fnbeh.2013.00217</a>","apa":"Dickerson, D., &#38; Bilkey, D. (2013). Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions. <i>Frontiers in Behavioral Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">https://doi.org/10.3389/fnbeh.2013.00217</a>","chicago":"Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.” <i>Frontiers in Behavioral Neuroscience</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fnbeh.2013.00217\">https://doi.org/10.3389/fnbeh.2013.00217</a>."},"date_published":"2013-12-27T00:00:00Z","department":[{"_id":"JoCs"}],"file":[{"creator":"system","date_created":"2018-12-12T10:15:10Z","content_type":"application/pdf","file_id":"5128","checksum":"cd7183121e56251176100ccac165c95c","file_size":530134,"relation":"main_file","access_level":"open_access","file_name":"IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf","date_updated":"2020-07-14T12:46:35Z"}],"oa_version":"Published Version","date_created":"2018-12-11T11:46:41Z","volume":7,"ddc":["571"],"file_date_updated":"2020-07-14T12:46:35Z","publication":"Frontiers in Behavioral Neuroscience","month":"12","language":[{"iso":"eng"}],"author":[{"id":"444EB89E-F248-11E8-B48F-1D18A9856A87","last_name":"Dickerson","first_name":"Desiree","full_name":"Dickerson, Desiree"},{"first_name":"David","full_name":"Bilkey, David","last_name":"Bilkey"}],"type":"journal_article","_id":"476","abstract":[{"text":"Maternal exposure to infection occurring mid-gestation produces a three-fold increase in the risk of schizophrenia in the offspring. The critical initiating factor appears to be the maternal immune activation (MIA) that follows infection. This process can be induced in rodents by exposure of pregnant dams to the viral mimic Poly I:C, which triggers an immune response that results in structural, functional, behavioral, and electrophysiological phenotypes in the adult offspring that model those seen in schizophrenia. We used this model to explore the role of synchronization in brain neural networks, a process thought to be dysfunctional in schizophrenia and previously associated with positive, negative, and cognitive symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced an impairment in long-range neural synchrony in adult offspring between two regions implicated in schizophrenia pathology; the hippocampus and the medial prefrontal cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the antipsychotic clozapine. MIA animals have previously been shown to have impaired pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits in animal models. Our data showed that deficits in synchrony were positively correlated with the impairments in PPI. Subsequent analysis of LFP activity during the PPI response also showed that reduced coupling between the mPFC and the hippocampus following processing of the pre-pulse was associated with reduced PPI. The ability of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology provides a useful platform from which to investigate the ontogeny of aberrant synchronous processes. Further, the way in which the model expresses translatable deficits such as aberrant synchrony and reduced PPI will allow researchers to explore novel intervention strategies targeted to these changes. ","lang":"eng"}],"publist_id":"7346","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Frontiers Research Foundation"},{"publist_id":"7321","date_published":"2013-01-04T00:00:00Z","publisher":"American Association for the Advancement of Science","oa_version":"None","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"499","quality_controlled":"1","abstract":[{"text":"Exposure of an isogenic bacterial population to a cidal antibiotic typically fails to eliminate a small fraction of refractory cells. Historically, fractional killing has been attributed to infrequently dividing or nondividing &quot;persisters.&quot; Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although persistence in these studies was characterized by stable numbers of cells, this apparent stability was actually a dynamic state of balanced division and death. Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic pulses that were negatively correlated with cell survival. These behaviors may reflect epigenetic effects, because KatG pulsing and death were correlated between sibling cells. Selection of lineages characterized by infrequent KatG pulsing could allow nonresponsive adaptation during prolonged drug exposure.","lang":"eng"}],"citation":{"ista":"Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115), 91–95.","ieee":"Y. Wakamoto <i>et al.</i>, “Dynamic persistence of antibiotic-stressed mycobacteria,” <i>Science</i>, vol. 339, no. 6115. American Association for the Advancement of Science, pp. 91–95, 2013.","short":"Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler, J. Mckinney, Science 339 (2013) 91–95.","mla":"Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>, vol. 339, no. 6115, American Association for the Advancement of Science, 2013, pp. 91–95, doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>.","chicago":"Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.” <i>Science</i>. American Association for the Advancement of Science, 2013. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>.","apa":"Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler, S., &#38; Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1229858\">https://doi.org/10.1126/science.1229858</a>","ama":"Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed mycobacteria. <i>Science</i>. 2013;339(6115):91-95. doi:<a href=\"https://doi.org/10.1126/science.1229858\">10.1126/science.1229858</a>"},"publication_status":"published","scopus_import":1,"intvolume":"       339","status":"public","publication":"Science","date_updated":"2021-01-12T08:01:06Z","type":"journal_article","month":"01","language":[{"iso":"eng"}],"author":[{"full_name":"Wakamoto, Yurichi","first_name":"Yurichi","last_name":"Wakamoto"},{"last_name":"Dhar","first_name":"Neraaj","full_name":"Dhar, Neraaj"},{"orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","first_name":"Remy P","full_name":"Chait, Remy P"},{"full_name":"Schneider, Katrin","first_name":"Katrin","last_name":"Schneider"},{"first_name":"François","full_name":"Signorino Gelo, François","last_name":"Signorino Gelo"},{"first_name":"Stanislas","full_name":"Leibler, Stanislas","last_name":"Leibler"},{"first_name":"John","full_name":"Mckinney, John","last_name":"Mckinney"}],"date_created":"2018-12-11T11:46:48Z","year":"2013","page":"91 - 95","day":"04","doi":"10.1126/science.1229858","title":"Dynamic persistence of antibiotic-stressed mycobacteria","issue":"6115","volume":339},{"oa":1,"intvolume":"        13","status":"public","date_updated":"2021-01-12T08:01:08Z","pubrep_id":"941","doi":"10.1186/1471-2148-13-222","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"222","day":"09","issue":"1","has_accepted_license":"1","title":"Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza","year":"2013","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:36Z","file_name":"IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf","relation":"main_file","access_level":"open_access","checksum":"52cf48a7c1794676ae8b0029573a84a9","file_size":1150052,"file_id":"4722","content_type":"application/pdf","date_created":"2018-12-12T10:08:59Z","creator":"system"}],"department":[{"_id":"JoBo"}],"date_published":"2013-10-09T00:00:00Z","citation":{"short":"M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary Biology 13 (2013).","mla":"Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, 222, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>.","ieee":"M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","ista":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology. 13(1), 222.","apa":"Ward, M., Lycett, S., Avila, D., Bollback, J. P., &#38; Leigh Brown, A. (2013). Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>","ama":"Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. <i>BMC Evolutionary Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-13-222\">10.1186/1471-2148-13-222</a>","chicago":"Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase in Avian Influenza.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-222\">https://doi.org/10.1186/1471-2148-13-222</a>."},"publication_status":"published","quality_controlled":"1","type":"journal_article","author":[{"last_name":"Ward","first_name":"Melissa","full_name":"Ward, Melissa"},{"full_name":"Lycett, Samantha","first_name":"Samantha","last_name":"Lycett"},{"full_name":"Avila, Dorita","first_name":"Dorita","last_name":"Avila"},{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Leigh Brown","full_name":"Leigh Brown, Andrew","first_name":"Andrew"}],"month":"10","language":[{"iso":"eng"}],"scopus_import":1,"publication":"BMC Evolutionary Biology","file_date_updated":"2020-07-14T12:46:36Z","volume":13,"ddc":["576"],"date_created":"2018-12-11T11:46:49Z","publisher":"BioMed Central","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7320","abstract":[{"text":"Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.","lang":"eng"}],"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council, the Government of the Republic of Panama, the Interdisciplinary Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC BY 2.0\r\n","_id":"500"},{"oa":1,"status":"public","intvolume":"        94","pubrep_id":"940","date_updated":"2021-01-12T08:01:09Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"day":"01","doi":"10.1644/12-MAMM-A-169.1","has_accepted_license":"1","issue":"6","title":"A new species of tapir from the Amazon","year":"2013","file":[{"date_updated":"2020-07-14T12:46:36Z","access_level":"open_access","relation":"main_file","file_size":1040765,"checksum":"8007815078dccac21ecd1cf73a269dc6","file_name":"IST-2018-940-v1+1_2013_Redondo_A_new.pdf","date_created":"2018-12-12T10:12:59Z","file_id":"4980","content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","department":[{"_id":"JoBo"}],"date_published":"2013-12-01T00:00:00Z","citation":{"ista":"Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of Mammalogy. 94(6), 1331–1345.","ieee":"M. Cozzuol <i>et al.</i>, “A new species of tapir from the Amazon,” <i>Journal of Mammalogy</i>, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.","mla":"Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” <i>Journal of Mammalogy</i>, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45, doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>.","short":"M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy, R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.","chicago":"Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A New Species of Tapir from the Amazon.” <i>Journal of Mammalogy</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>.","apa":"Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy, B., … Santos, F. (2013). A new species of tapir from the Amazon. <i>Journal of Mammalogy</i>. Oxford University Press. <a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">https://doi.org/10.1644/12-MAMM-A-169.1</a>","ama":"Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon. <i>Journal of Mammalogy</i>. 2013;94(6):1331-1345. doi:<a href=\"https://doi.org/10.1644/12-MAMM-A-169.1\">10.1644/12-MAMM-A-169.1</a>"},"publication_status":"published","quality_controlled":"1","author":[{"first_name":"Mario","full_name":"Cozzuol, Mario","last_name":"Cozzuol"},{"first_name":"Camila","full_name":"Clozato, Camila","last_name":"Clozato"},{"last_name":"Holanda","full_name":"Holanda, Elizete","first_name":"Elizete"},{"first_name":"Flávio","full_name":"Rodrigues, Flávio","last_name":"Rodrigues"},{"last_name":"Nienow","first_name":"Samuel","full_name":"Nienow, Samuel"},{"first_name":"Benoit","full_name":"De Thoisy, Benoit","last_name":"De Thoisy"},{"orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","first_name":"Rodrigo A","last_name":"Fernandes Redondo"},{"last_name":"Santos","first_name":"Fabrício","full_name":"Santos, Fabrício"}],"month":"12","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":1,"publication":"Journal of Mammalogy","ddc":["570"],"volume":94,"file_date_updated":"2020-07-14T12:46:36Z","date_created":"2018-12-11T11:46:49Z","page":"1331 - 1345","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7319","abstract":[{"text":"All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.","lang":"eng"}],"_id":"501"},{"date_updated":"2021-01-12T08:01:09Z","publication":"Journal of Computer Security","scopus_import":1,"intvolume":"        21","status":"public","type":"journal_article","author":[{"last_name":"Blazy","full_name":"Blazy, Olivier","first_name":"Olivier"},{"last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pointcheval","first_name":"David","full_name":"Pointcheval, David"},{"last_name":"Vergnaud","first_name":"Damien","full_name":"Vergnaud, Damien"}],"month":"11","language":[{"iso":"eng"}],"page":"627 - 661","date_created":"2018-12-11T11:46:50Z","year":"2013","title":"Short blind signatures","issue":"5","volume":21,"day":"22","doi":"10.3233/JCS-130477","date_published":"2013-11-22T00:00:00Z","publist_id":"7318","department":[{"_id":"KrPi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publisher":"IOS Press","quality_controlled":"1","_id":"502","abstract":[{"text":"Blind signatures allow users to obtain signatures on messages hidden from the signer; moreover, the signer cannot link the resulting message/signature pair to the signing session. This paper presents blind signature schemes, in which the number of interactions between the user and the signer is minimal and whose blind signatures are short. Our schemes are defined over bilinear groups and are proved secure in the common-reference-string model without random oracles and under standard assumptions: CDH and the decision-linear assumption. (We also give variants over asymmetric groups based on similar assumptions.) The blind signatures are Waters signatures, which consist of 2 group elements. Moreover, we instantiate partially blind signatures, where the message consists of a part hidden from the signer and a commonly known public part, and schemes achieving perfect blindness. We propose new variants of blind signatures, such as signer-friendly partially blind signatures, where the public part can be chosen by the signer without prior agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated messages provided by independent sources. We also extend Waters signatures to non-binary alphabets by proving a new result on the underlying hash function. ","lang":"eng"}],"publication_status":"published","citation":{"chicago":"Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud. “Short Blind Signatures.” <i>Journal of Computer Security</i>. IOS Press, 2013. <a href=\"https://doi.org/10.3233/JCS-130477\">https://doi.org/10.3233/JCS-130477</a>.","apa":"Blazy, O., Fuchsbauer, G., Pointcheval, D., &#38; Vergnaud, D. (2013). Short blind signatures. <i>Journal of Computer Security</i>. IOS Press. <a href=\"https://doi.org/10.3233/JCS-130477\">https://doi.org/10.3233/JCS-130477</a>","ama":"Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. <i>Journal of Computer Security</i>. 2013;21(5):627-661. doi:<a href=\"https://doi.org/10.3233/JCS-130477\">10.3233/JCS-130477</a>","ista":"Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures. Journal of Computer Security. 21(5), 627–661.","short":"O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer Security 21 (2013) 627–661.","mla":"Blazy, Olivier, et al. “Short Blind Signatures.” <i>Journal of Computer Security</i>, vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:<a href=\"https://doi.org/10.3233/JCS-130477\">10.3233/JCS-130477</a>.","ieee":"O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,” <i>Journal of Computer Security</i>, vol. 21, no. 5. IOS Press, pp. 627–661, 2013."}},{"scopus_import":1,"intvolume":"        15","status":"public","date_updated":"2021-01-12T08:01:11Z","publication":"Green Chemistry","type":"journal_article","month":"02","author":[{"last_name":"Greimel","full_name":"Greimel, Katrin","first_name":"Katrin"},{"first_name":"Veronika","full_name":"Perz, Veronika","last_name":"Perz"},{"full_name":"Koren, Klaus","first_name":"Klaus","last_name":"Koren","id":"382FBD6A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roland","full_name":"Feola, Roland","last_name":"Feola"},{"first_name":"Armin","full_name":"Temel, Armin","last_name":"Temel"},{"first_name":"Christian","full_name":"Sohar, Christian","last_name":"Sohar"},{"full_name":"Herrero Acero, Enrique","first_name":"Enrique","last_name":"Herrero Acero"},{"first_name":"Ingo","full_name":"Klimant, Ingo","last_name":"Klimant"},{"last_name":"Guebitz","full_name":"Guebitz, Georg","first_name":"Georg"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:51Z","year":"2013","page":"381 - 388","doi":"10.1039/c2gc36666e","day":"01","title":"Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins","issue":"2","volume":15,"publist_id":"7313","date_published":"2013-02-01T00:00:00Z","oa_version":"None","publisher":"Royal Society of Chemistry","department":[{"_id":"HaJa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This study was performed within the Austrian Centre of Indus-\r\ntrial Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology  Agency  of  the  City  of  Vienna  through  the\r\nCOMET-Funding Program managed by the Austrian Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with the CLSM measurements.","_id":"505","quality_controlled":"1","abstract":[{"text":"Alkyd resins are polyesters containing unsaturated fatty acids that are used as binding agents in paints and coatings. Chemical drying of these polyesters is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective, yet they have been proven to be carcinogenic. Therefore, strategies to replace the cobalt-based catalyst by environmentally friendlier and less toxic alternatives are under development. Here, we demonstrate for the first time that a laccase-mediator system can effectively replace the heavy-metal catalyst and cross-link alkyd resins. Interestingly, the biocatalytic reaction does not only work in aqueous media, but also in a solid film, where enzyme diffusion is limited. Within the catalytic cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase, which is uniformly distributed within the drying film as evidenced by confocal laser scanning microscopy. During gradual build-up of molecular weight, there is a concomitant decrease of the oxygen content in the film. A new optical sensor to follow oxygen consumption during the cross-linking reaction was developed and validated with state of the art techniques. A remarkable feature is the low sample amount required, which allows faster screening of new catalysts.","lang":"eng"}],"publication_status":"published","citation":{"ieee":"K. Greimel <i>et al.</i>, “Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins,” <i>Green Chemistry</i>, vol. 15, no. 2. Royal Society of Chemistry, pp. 381–388, 2013.","mla":"Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” <i>Green Chemistry</i>, vol. 15, no. 2, Royal Society of Chemistry, 2013, pp. 381–88, doi:<a href=\"https://doi.org/10.1039/c2gc36666e\">10.1039/c2gc36666e</a>.","short":"K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero, I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388.","ista":"Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.","apa":"Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz, G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. <i>Green Chemistry</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c2gc36666e\">https://doi.org/10.1039/c2gc36666e</a>","ama":"Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of alkyd resins. <i>Green Chemistry</i>. 2013;15(2):381-388. doi:<a href=\"https://doi.org/10.1039/c2gc36666e\">10.1039/c2gc36666e</a>","chicago":"Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel, Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.” <i>Green Chemistry</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c2gc36666e\">https://doi.org/10.1039/c2gc36666e</a>."}},{"oa":1,"external_id":{"pmid":["23975898"]},"date_updated":"2021-01-12T08:01:12Z","status":"public","intvolume":"        25","title":"Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis","issue":"8","doi":"10.1105/tpc.113.114264","day":"01","year":"2013","department":[{"_id":"JiFr"}],"oa_version":"Submitted Version","date_published":"2013-08-01T00:00:00Z","publication_status":"published","citation":{"ista":"Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985.","short":"S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml, G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.","mla":"Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>.","ieee":"S. Kim <i>et al.</i>, “Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.","chicago":"Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt, Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>.","ama":"Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. 2013;25(8):2970-2985. doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>","apa":"Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013). Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>"},"quality_controlled":"1","month":"08","language":[{"iso":"eng"}],"author":[{"last_name":"Kim","full_name":"Kim, Soo","first_name":"Soo"},{"last_name":"Xu","full_name":"Xu, Zheng","first_name":"Zheng"},{"last_name":"Song","first_name":"Kyungyoung","full_name":"Song, Kyungyoung"},{"last_name":"Kim","first_name":"Dae","full_name":"Kim, Dae"},{"full_name":"Kang, Hyangju","first_name":"Hyangju","last_name":"Kang"},{"last_name":"Reichardt","full_name":"Reichardt, Ilka","first_name":"Ilka"},{"first_name":"Eun","full_name":"Sohn, Eun","last_name":"Sohn"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Gerd","full_name":"Juergens, Gerd","last_name":"Juergens"},{"first_name":"Inhwan","full_name":"Hwang, Inhwan","last_name":"Hwang"}],"type":"journal_article","publication":"Plant Cell","scopus_import":1,"volume":25,"page":"2970 - 2985","date_created":"2018-12-11T11:46:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Society of Plant Biologists","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/","open_access":"1"}],"publist_id":"7312","abstract":[{"text":"Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs.","lang":"eng"}],"pmid":1,"_id":"507"},{"publisher":"Oxford University Press","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7310","abstract":[{"lang":"eng","text":"The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases."}],"_id":"508","pmid":1,"month":"09","language":[{"iso":"eng"}],"author":[{"first_name":"Eduardo","full_name":"Tarazona Santos, Eduardo","last_name":"Tarazona Santos"},{"first_name":"Moara","full_name":"Machado, Moara","last_name":"Machado"},{"first_name":"Wagner","full_name":"Magalhães, Wagner","last_name":"Magalhães"},{"last_name":"Chen","first_name":"Renee","full_name":"Chen, Renee"},{"full_name":"Lyon, Fernanda","first_name":"Fernanda","last_name":"Lyon"},{"full_name":"Burdett, Laurie","first_name":"Laurie","last_name":"Burdett"},{"first_name":"Andrew","full_name":"Crenshaw, Andrew","last_name":"Crenshaw"},{"full_name":"Fabbri, Cristina","first_name":"Cristina","last_name":"Fabbri"},{"full_name":"Pereira, Latife","first_name":"Latife","last_name":"Pereira"},{"full_name":"Pinto, Laelia","first_name":"Laelia","last_name":"Pinto"},{"first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793"},{"first_name":"Ben","full_name":"Sestanovich, Ben","last_name":"Sestanovich"},{"first_name":"Meredith","full_name":"Yeager, Meredith","last_name":"Yeager"},{"last_name":"Chanock","first_name":"Stephen","full_name":"Chanock, Stephen"}],"type":"journal_article","scopus_import":1,"publication":"Molecular Biology and Evolution","volume":30,"date_created":"2018-12-11T11:46:52Z","page":"2157 - 2167","oa_version":"Submitted Version","department":[{"_id":"JoBo"}],"date_published":"2013-09-01T00:00:00Z","citation":{"chicago":"Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen, Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>.","ama":"Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. <i>Molecular Biology and Evolution</i>. 2013;30(9):2157-2167. doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>","apa":"Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett, L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/mst119\">https://doi.org/10.1093/molbev/mst119</a>","ista":"Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M, Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution. 30(9), 2157–2167.","ieee":"E. Tarazona Santos <i>et al.</i>, “Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9. Oxford University Press, pp. 2157–2167, 2013.","mla":"Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” <i>Molecular Biology and Evolution</i>, vol. 30, no. 9, Oxford University Press, 2013, pp. 2157–67, doi:<a href=\"https://doi.org/10.1093/molbev/mst119\">10.1093/molbev/mst119</a>.","short":"E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett, A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich, M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167."},"publication_status":"published","quality_controlled":"1","external_id":{"pmid":["23821607"]},"oa":1,"status":"public","intvolume":"        30","date_updated":"2021-01-12T08:01:12Z","day":"01","doi":"10.1093/molbev/mst119","title":"Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications","issue":"9","year":"2013"}]